| f0a97bb | Fabien Campagne | 09 June 2012, 20:33:38 UTC | fix case of the version filename. | 09 June 2012, 20:36:38 UTC |
| 5980775 | Fabien Campagne | 09 June 2012, 20:25:11 UTC | Version mode will display the content of Version.txt from the jar file. The release file creates the Version.txt file with the tag, and goby-jar now puts the file in the jar file. java -jar goby.jar -m v will now print: Goby Version: 2.0 (20120609162251) | 09 June 2012, 20:25:11 UTC |
| bfa0aa7 | Fabien Campagne | 09 June 2012, 19:34:52 UTC | adjust symbolic links for new tag scheme. | 09 June 2012, 19:47:49 UTC |
| 4961bd4 | Fabien Campagne | 09 June 2012, 19:09:40 UTC | Prefix archive filenames with goby_ so the tag can simply be 2.0 | 09 June 2012, 19:09:40 UTC |
| cb92548 | Fabien Campagne | 09 June 2012, 18:19:07 UTC | Update build support revision. | 09 June 2012, 19:08:32 UTC |
| 9b3ee13 | Fabien Campagne | 09 June 2012, 18:27:00 UTC | exclude .git repository when copying submodules. | 09 June 2012, 19:05:23 UTC |
| 9a63b6f | Fabien Campagne | 09 June 2012, 18:36:40 UTC | update buildsupport revision. | 09 June 2012, 19:05:00 UTC |
| 75bbd1c | Fabien Campagne | 09 June 2012, 19:03:33 UTC | Merge branch 'master' of github.com:CampagneLaboratory/goby | 09 June 2012, 19:03:33 UTC |
| 93d7a21 | Fabien Campagne | 09 June 2012, 18:53:55 UTC | merged from RC2 | 09 June 2012, 19:03:06 UTC |
| 5f28745 | Fabien Campagne | 09 June 2012, 18:19:07 UTC | Provide checkout and building instructions. | 09 June 2012, 18:19:07 UTC |
| d351e93 | Fabien Campagne | 09 June 2012, 17:13:06 UTC | Fix permission on git-export.sh | 09 June 2012, 17:13:06 UTC |
| 75ae25e | Fabien Campagne | 09 June 2012, 16:40:08 UTC | buildsupport version with support for git | 09 June 2012, 16:40:08 UTC |
| 399bf18 | Fabien Campagne | 09 June 2012, 16:20:09 UTC | Make it possible to release from Git. When the property use-git is set, we use the GitRepository to prepare a release. A tag is made (but not pushed to remote). After a release is successful, you need the push the tag to GitHub. | 09 June 2012, 16:20:09 UTC |
| c2198cb | Fabien Campagne | 08 June 2012, 21:49:35 UTC | Kevin's fix for concatenate-reads, which previously failed to concat the paired fields of a read. | 08 June 2012, 21:49:35 UTC |
| a89f931 | Fabien Campagne | 08 June 2012, 19:35:09 UTC | Bring Git in sync with SVN Head before disabling SVN HEAD for commits. | 08 June 2012, 19:35:09 UTC |
| bd3ab9b | Fabien Campagne | 08 June 2012, 17:30:06 UTC | Run GZip codec at best speed rather than best compression. Compression appears similar, but much faster. | 08 June 2012, 17:30:06 UTC |
| 0c42bae | Fabien Campagne | 08 June 2012, 17:23:53 UTC | Additional TMH merge optimization. | 08 June 2012, 17:24:11 UTC |
| fe55482 | Fabien Campagne | 08 June 2012, 14:49:23 UTC | Optimize TMH writer. | 08 June 2012, 14:49:23 UTC |
| 5445d22 | Fabien Campagne | 07 June 2012, 20:33:16 UTC | Use an AVLTreeSet when merging TMH. | 07 June 2012, 20:33:29 UTC |
| 772ae1d | Fabien Campagne | 07 June 2012, 20:29:45 UTC | change permissions on some files. Last idea ipr project. | 07 June 2012, 20:29:45 UTC |
| 705c002 | Fabien Campagne | 07 June 2012, 20:29:04 UTC | fix min max query index issues, that led to incorrect query number for some recent alignments. | 07 June 2012, 20:29:04 UTC |
| 4b9bc6b | Fabien Campagne | 07 June 2012, 17:46:31 UTC | Avoid a lot of garbage collection by reusing objects for run length encoding. Optimize encoding/decoding for compact lists of symbols. | 07 June 2012, 17:49:47 UTC |
| 0ffa426 | Fabien Campagne | 06 June 2012, 15:41:10 UTC | Add .gitignore | 06 June 2012, 15:41:10 UTC |
| 1af4220 | Fabien Campagne | 06 June 2012, 15:36:54 UTC | Fix ling endings again | 06 June 2012, 15:36:54 UTC |
| 4855f9b | Fabien Campagne | 06 June 2012, 15:33:58 UTC | Remove vcxproj files. Fix line endings again.. | 06 June 2012, 15:33:58 UTC |
| a9134b3 | Fabien Campagne | 06 June 2012, 13:50:55 UTC | Remove limit on PB chunks for alignment data. | 06 June 2012, 15:13:51 UTC |
| 9bb934a | Fabien Campagne | 05 June 2012, 17:41:50 UTC | Fix ling endings. | 05 June 2012, 17:41:50 UTC |
| c1b0344 | Fabien Campagne | 05 June 2012, 17:34:43 UTC | Remove read strand info from pairFlag (already stored in its own field) and put it back when we decompress. | 05 June 2012, 17:36:25 UTC |
| 988bb34 | Fabien Campagne | 04 June 2012, 16:38:33 UTC | commit latest changes | 04 June 2012, 16:38:33 UTC |
| 48cf845 | Fabien Campagne | 04 June 2012, 15:22:53 UTC | rename attribute to preserve-read-names | 04 June 2012, 16:37:29 UTC |
| bf84832 | Fabien Campagne | 03 June 2012, 16:34:52 UTC | update .gitattributes | 03 June 2012, 16:34:52 UTC |
| 39d9ba0 | Fabien Campagne | 02 June 2012, 16:22:37 UTC | add fasta/fastq file types | 02 June 2012, 16:22:37 UTC |
| 43054c1 | Fabien Campagne | 02 June 2012, 15:40:22 UTC | normalize line endings | 02 June 2012, 15:40:31 UTC |
| a8abdfe | Fabien Campagne | 02 June 2012, 15:24:34 UTC | Define .gitattributes for line endings | 02 June 2012, 15:24:34 UTC |
| 2e56d10 | Fabien Campagne | 02 June 2012, 14:54:22 UTC | Adding submodules buildsupport and testsupport | 02 June 2012, 14:54:22 UTC |
| b55649e | Kevin C. Dorf | 01 June 2012, 20:56:53 UTC | fix input location git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/campagnelab/goby/trunk@32170 60cd2ccc-2b05-0410-9566-da273a940bff | 01 June 2012, 20:56:53 UTC |
| 1ee67c8 | Kevin C. Dorf | 01 June 2012, 20:35:53 UTC | Round trip tests for all 10 tags, first 5000 alignments of each. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/campagnelab/goby/trunk@32169 60cd2ccc-2b05-0410-9566-da273a940bff | 01 June 2012, 20:35:53 UTC |
| d23f8eb | Fabien Campagne | 01 June 2012, 19:12:48 UTC | Fix Quick concat bug reported by Zachary Zeno git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/campagnelab/goby/trunk@32161 60cd2ccc-2b05-0410-9566-da273a940bff | 01 June 2012, 19:12:48 UTC |
| f799112 | Fabien Campagne | 31 May 2012, 19:33:53 UTC | Move to new SVN organization before svn2git import git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/campagnelab/goby/trunk@32134 60cd2ccc-2b05-0410-9566-da273a940bff | 31 May 2012, 19:33:53 UTC |
| 0bacf50 | Fabien Campagne | 31 May 2012, 19:33:41 UTC | undo git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@32133 60cd2ccc-2b05-0410-9566-da273a940bff | 31 May 2012, 19:33:41 UTC |
| f3d2661 | Fabien Campagne | 31 May 2012, 19:33:05 UTC | Move to new SVN organization before svn2git import git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/campagnelab/goby/trunk/goby@32132 60cd2ccc-2b05-0410-9566-da273a940bff | 31 May 2012, 19:33:05 UTC |
| 2b2c9cd | Kevin C. Dorf | 31 May 2012, 18:14:51 UTC | * Always save samflags when converting sam-to-compact * Fix an issue related to when using predefined quals are kept in spliced reads with compact-to-sam. * Option to preserve reads names when going sam-to-compact. If they are kept in the compact file, they will be written to the compact-to-sam file, as well * Make test comparison and SamComparisonMode friendlier with sam/cram files where both expected and actual might contain unmapped reads * Improve the scoring system in SamComparison so some options are weighted more than others on a comparison failure * SamPerPositionComparison is now smarter since it can use readNames to determine with items pair up at a position git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@32127 60cd2ccc-2b05-0410-9566-da273a940bff | 31 May 2012, 18:14:51 UTC |
| 8ec5622 | Fabien Campagne | 31 May 2012, 17:02:23 UTC | new trunk git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/campagnelab/goby/trunk@32061 60cd2ccc-2b05-0410-9566-da273a940bff | 31 May 2012, 17:02:23 UTC |
| 39b0400 | Fabien Campagne | 31 May 2012, 15:49:34 UTC | Expand description. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@32057 60cd2ccc-2b05-0410-9566-da273a940bff | 31 May 2012, 15:49:34 UTC |
| fa77547 | Fabien Campagne | 30 May 2012, 23:16:20 UTC | Add README.md git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@32054 60cd2ccc-2b05-0410-9566-da273a940bff | 30 May 2012, 23:16:20 UTC |
| 0dfe264 | Kevin C. Dorf | 30 May 2012, 18:50:27 UTC | add read name from protobuf generated classes git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@32050 60cd2ccc-2b05-0410-9566-da273a940bff | 30 May 2012, 18:50:27 UTC |
| 4ac1340 | Kevin C. Dorf | 30 May 2012, 18:46:10 UTC | optional read name for alignment entries. useful for to/from bam, especially in tests. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@32047 60cd2ccc-2b05-0410-9566-da273a940bff | 30 May 2012, 18:46:10 UTC |
| 5c73c22 | Fabien Campagne | 29 May 2012, 21:20:52 UTC | Disable tests that will not run on server. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@32040 60cd2ccc-2b05-0410-9566-da273a940bff | 29 May 2012, 21:20:52 UTC |
| 14a9b94 | Kevin C. Dorf | 29 May 2012, 21:14:39 UTC | Fix Sam comparison to put compare in the right place git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@32036 60cd2ccc-2b05-0410-9566-da273a940bff | 29 May 2012, 21:14:39 UTC |
| 7cd3f1d | Fabien Campagne | 29 May 2012, 20:47:50 UTC | Transfer recent changes from RC branch back to Goby main trunk. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@32032 60cd2ccc-2b05-0410-9566-da273a940bff | 29 May 2012, 20:47:50 UTC |
| 1ba1220 | Kevin C. Dorf | 29 May 2012, 18:17:12 UTC | Test sample quality mode with both known fastq and fasta git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@32017 60cd2ccc-2b05-0410-9566-da273a940bff | 29 May 2012, 18:17:12 UTC |
| f9766b8 | Kevin C. Dorf | 29 May 2012, 17:24:57 UTC | * Fix reporting of errors on fields where there is no actual different between the fields in the "best match" for a position. * SampleQualityScores can report if no quality scores are found (it will report the likely encoding as 'fasta'). git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@32014 60cd2ccc-2b05-0410-9566-da273a940bff | 29 May 2012, 17:24:57 UTC |
| 1234822 | Fabien Campagne | 25 May 2012, 16:59:47 UTC | Transfer recent changes from RC branch back to Goby main trunk. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31978 60cd2ccc-2b05-0410-9566-da273a940bff | 25 May 2012, 16:59:47 UTC |
| 8fd77bc | Fabien Campagne | 22 May 2012, 23:10:22 UTC | Recent changes on release candidate branch (support for quality scores on soft-clips, group associations support in vcf parsers/writers). Fixing a bug reported by Zachary Zeno in ReadsReader.decodeQuality score when there is no quality scores. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31942 60cd2ccc-2b05-0410-9566-da273a940bff | 22 May 2012, 23:10:22 UTC |
| b9629cf | Kevin C. Dorf | 22 May 2012, 19:06:28 UTC | change queryIndexes to unsigned int all around. Observe each queryIndex without respect to if it aligned or not. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31934 60cd2ccc-2b05-0410-9566-da273a940bff | 22 May 2012, 19:06:28 UTC |
| 2f48691 | Fabien Campagne | 22 May 2012, 17:22:22 UTC | Bug fix contributed by Zachary Zeno. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31933 60cd2ccc-2b05-0410-9566-da273a940bff | 22 May 2012, 17:22:22 UTC |
| 7957a10 | Fabien Campagne | 18 May 2012, 23:05:06 UTC | Change output to TSV and make several independent files, one per type of data. Now also observe depths independently of fragments. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31916 60cd2ccc-2b05-0410-9566-da273a940bff | 18 May 2012, 23:05:06 UTC |
| 8d42e94 | Fabien Campagne | 18 May 2012, 23:04:25 UTC | Change output to TSV and make several independent files, one per type of data. Now also observe depths independently of fragments. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31915 60cd2ccc-2b05-0410-9566-da273a940bff | 18 May 2012, 23:04:25 UTC |
| 15dbcdb | Fabien Campagne | 18 May 2012, 15:24:17 UTC | update project git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31908 60cd2ccc-2b05-0410-9566-da273a940bff | 18 May 2012, 15:24:17 UTC |
| 93692dd | Kevin C. Dorf | 17 May 2012, 20:20:01 UTC | Improved comparison based on details found in JRO, notably when bases in the reference may be lowercase git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31903 60cd2ccc-2b05-0410-9566-da273a940bff | 17 May 2012, 20:20:01 UTC |
| 0d62d7c | Fabien Campagne | 17 May 2012, 19:38:15 UTC | AlignmentEntry field insertSize is now stored in protobuf with sint32 rather than uint32 since negative values can be stored in this field. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31900 60cd2ccc-2b05-0410-9566-da273a940bff | 17 May 2012, 19:38:15 UTC |
| 421b9ab | Kevin C. Dorf | 17 May 2012, 19:11:08 UTC | build sequence cache is now tolerant of lowercase bases git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31898 60cd2ccc-2b05-0410-9566-da273a940bff | 17 May 2012, 19:11:08 UTC |
| 68852bd | Kevin C. Dorf | 17 May 2012, 17:14:59 UTC | * Improved comparison when comparing sam records (per position) * Fixed choice target index on writing sam from compact * Removed commons pool as it isn't used by anything * Fix problem with writing targets in sam-to-compact and added test * Fix numerous things that idea complained about git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31892 60cd2ccc-2b05-0410-9566-da273a940bff | 17 May 2012, 17:14:59 UTC |
| 656cca8 | Fabien Campagne | 16 May 2012, 18:56:05 UTC | Do not store insert size because this is a value that can be calculated from the read and mate positions. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31882 60cd2ccc-2b05-0410-9566-da273a940bff | 16 May 2012, 18:56:05 UTC |
| 51d401d | Fabien Campagne | 16 May 2012, 17:02:32 UTC | Support multiple group comparisons for RNA-Seq diff exp (mode compact-alignment-to-annotation-counts). git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31880 60cd2ccc-2b05-0410-9566-da273a940bff | 16 May 2012, 17:02:32 UTC |
| b144cf1 | Fabien Campagne | 15 May 2012, 22:47:12 UTC | we only store the full quality score on the first entry with a given query index. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31869 60cd2ccc-2b05-0410-9566-da273a940bff | 15 May 2012, 22:47:12 UTC |
| aabb280 | Fabien Campagne | 15 May 2012, 22:19:48 UTC | Fix test. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31867 60cd2ccc-2b05-0410-9566-da273a940bff | 15 May 2012, 22:19:48 UTC |
| 905bc9c | Fabien Campagne | 15 May 2012, 22:19:33 UTC | Store read quality scores, then remove from result before checking for template compression. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31866 60cd2ccc-2b05-0410-9566-da273a940bff | 15 May 2012, 22:19:33 UTC |
| ae287b9 | Fabien Campagne | 15 May 2012, 21:54:45 UTC | Set the number of query sequences correctly. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31864 60cd2ccc-2b05-0410-9566-da273a940bff | 15 May 2012, 21:54:45 UTC |
| 0f35ce4 | Fabien Campagne | 15 May 2012, 21:33:08 UTC | Update the value of the variable before printing. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31863 60cd2ccc-2b05-0410-9566-da273a940bff | 15 May 2012, 21:33:08 UTC |
| 9a54491 | Fabien Campagne | 15 May 2012, 19:15:19 UTC | document. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31861 60cd2ccc-2b05-0410-9566-da273a940bff | 15 May 2012, 19:15:19 UTC |
| ac52558 | Fabien Campagne | 15 May 2012, 19:00:35 UTC | We had a problem with the calculation of numQueryIndices when adjustQueryIndex is false. In this case, we need to take the max of numQueryIndices across reader rather than summing the number across readers. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31858 60cd2ccc-2b05-0410-9566-da273a940bff | 15 May 2012, 19:00:35 UTC |
| 1a1f3e5 | Fabien Campagne | 15 May 2012, 18:57:49 UTC | It turns out that GZipOutputStream uses a different compression level on linux and macOs (best compression on linux, faster on mac). For Goby, we really always want best compression, so we subclass GZipOutputStream to set the level explicitly. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31857 60cd2ccc-2b05-0410-9566-da273a940bff | 15 May 2012, 18:57:49 UTC |
| 9f4d1da | Fabien Campagne | 15 May 2012, 18:18:26 UTC | Fix the criterion that determines if the merge is the last one. Fix the calculation of the range for the merge result. Delete the splits in tmp when the JVM exits. Add a --dry-run option useful to see what will happen without actually doing anything. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31856 60cd2ccc-2b05-0410-9566-da273a940bff | 15 May 2012, 18:18:26 UTC |
| a789a02 | Fabien Campagne | 15 May 2012, 16:10:23 UTC | Do not upgrade alignment when byte offsets are given to the reader constructor. This improves performance of sort dramatically. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31855 60cd2ccc-2b05-0410-9566-da273a940bff | 15 May 2012, 16:10:23 UTC |
| 1086b2a | Fabien Campagne | 15 May 2012, 15:24:11 UTC | Try to put something in this collection to help the linux implementation of BZip2 avoid a divide by zero.: java.lang.ArithmeticException: / by zero at org.apache.tools.bzip2.CBZip2OutputStream.mainSort(CBZip2OutputStream.java:1173) at org.apache.tools.bzip2.CBZip2OutputStream.doReversibleTransformation(CBZip2OutputStream.java:1385) at org.apache.tools.bzip2.CBZip2OutputStream.endBlock(CBZip2OutputStream.java:476) at org.apache.tools.bzip2.CBZip2OutputStream.close(CBZip2OutputStream.java:427) at edu.cornell.med.icb.goby.compression.BZip2ChunkCodec.encode(BZip2ChunkCodec.java:82) at edu.cornell.med.icb.goby.compression.TestBZip2ChunkCodec.roundTrip(TestBZip2ChunkCodec.java:44) git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31852 60cd2ccc-2b05-0410-9566-da273a940bff | 15 May 2012, 15:24:11 UTC |
| e07be95 | Fabien Campagne | 15 May 2012, 14:49:18 UTC | Fix the test. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31849 60cd2ccc-2b05-0410-9566-da273a940bff | 15 May 2012, 14:49:18 UTC |
| 406079d | Fabien Campagne | 14 May 2012, 21:34:13 UTC | Try to fix problem with empirical-p for regions. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31847 60cd2ccc-2b05-0410-9566-da273a940bff | 14 May 2012, 21:34:13 UTC |
| 73a48b2 | Fabien Campagne | 14 May 2012, 19:17:51 UTC | Merge back the changes made on RC2 branch into the trunk. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31844 60cd2ccc-2b05-0410-9566-da273a940bff | 14 May 2012, 19:17:51 UTC |
| 63e4963 | Fabien Campagne | 14 May 2012, 18:36:03 UTC | New binning strategies for empirical-stats + chi-square stat. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31842 60cd2ccc-2b05-0410-9566-da273a940bff | 14 May 2012, 18:36:03 UTC |
| f79f2b3 | Fabien Campagne | 11 May 2012, 22:29:40 UTC | Also fix the precision of p-values and MR for regions. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31821 60cd2ccc-2b05-0410-9566-da273a940bff | 11 May 2012, 22:29:40 UTC |
| f2c28f3 | Fabien Campagne | 11 May 2012, 22:15:59 UTC | VCFWriter: add methods to format double and floats. MethylationRateVCFOutput now writes P-values and other float numbers up to some reasonable number of digits after the decimal points. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31819 60cd2ccc-2b05-0410-9566-da273a940bff | 11 May 2012, 22:15:59 UTC |
| b06388e | Kevin C. Dorf | 11 May 2012, 20:47:39 UTC | C++/python versions set to 2.0.0 git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31817 60cd2ccc-2b05-0410-9566-da273a940bff | 11 May 2012, 20:47:39 UTC |
| c83cab6 | Kevin C. Dorf | 11 May 2012, 20:12:52 UTC | * switch back sort-1 and sort so sort is the split/merge sort now * progress loggers added to sort mode * SamComparison now has an interface and a 2nd implementation (well, extension really) that does comparison for all records at a specific position and then tries to figure out which of the records line up and compares those. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31816 60cd2ccc-2b05-0410-9566-da273a940bff | 11 May 2012, 20:12:52 UTC |
| c84eca1 | Fabien Campagne | 11 May 2012, 13:43:09 UTC | Now correctly checks if the seek position is outside the slice of interest. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31814 60cd2ccc-2b05-0410-9566-da273a940bff | 11 May 2012, 13:43:09 UTC |
| c0b89dc | Fabien Campagne | 10 May 2012, 23:23:27 UTC | Avoid going back in the input stream to validate codec stream. Add a class that was missing and caused IGV to fail. Validation bug fixed for hybrid. We should not use the stream.available() method to determine the remaining size left in the stream, it only indicates the number of bytes that can be returned without blocking (which is rather low when loading from URLs). Print the exceptions in sort. Catch negative array size exception (not sure yet what is wrong with the file that triggers that and assume no entries in chunk). git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31812 60cd2ccc-2b05-0410-9566-da273a940bff | 10 May 2012, 23:23:27 UTC |
| 2092b57 | Fabien Campagne | 10 May 2012, 18:07:03 UTC | Add some tests and really fix the validate method for Bzip2 and hybrid. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31807 60cd2ccc-2b05-0410-9566-da273a940bff | 10 May 2012, 18:07:03 UTC |
| f8428a1 | Kevin C. Dorf | 10 May 2012, 17:33:50 UTC | misplaced help closing tag git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31806 60cd2ccc-2b05-0410-9566-da273a940bff | 10 May 2012, 17:33:50 UTC |
| 2858477 | Fabien Campagne | 10 May 2012, 16:17:33 UTC | Add option --hi-c to merge compact alignments from pairs sequenced after the Hi-C protocol. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31802 60cd2ccc-2b05-0410-9566-da273a940bff | 10 May 2012, 16:17:33 UTC |
| 28e016f | Fabien Campagne | 10 May 2012, 16:15:58 UTC | Class needed by HiC Merge. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31801 60cd2ccc-2b05-0410-9566-da273a940bff | 10 May 2012, 16:15:58 UTC |
| 3ebfadf | Fabien Campagne | 10 May 2012, 16:13:17 UTC | Add methods on AlignmentWriter interface. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31800 60cd2ccc-2b05-0410-9566-da273a940bff | 10 May 2012, 16:13:17 UTC |
| 7b8fc14 | Fabien Campagne | 10 May 2012, 16:11:04 UTC | Improve documentation. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31799 60cd2ccc-2b05-0410-9566-da273a940bff | 10 May 2012, 16:11:04 UTC |
| 5406667 | Fabien Campagne | 10 May 2012, 16:04:58 UTC | Fix for validation of codec content. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31797 60cd2ccc-2b05-0410-9566-da273a940bff | 10 May 2012, 16:04:58 UTC |
| faf346b | Kevin C. Dorf | 10 May 2012, 16:04:49 UTC | Sort defaults to 30 files per merge and scaling factor of 100 in all places in java and jsap. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31796 60cd2ccc-2b05-0410-9566-da273a940bff | 10 May 2012, 16:04:49 UTC |
| 79c2f66 | Fabien Campagne | 10 May 2012, 11:32:47 UTC | Add tests and data file for hybrid codec. Tests currently fail because codec code is written in a place that reposition() does not expect. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31751 60cd2ccc-2b05-0410-9566-da273a940bff | 10 May 2012, 11:32:47 UTC |
| 4eee36f | Fabien Campagne | 10 May 2012, 10:34:06 UTC | If the codec could not validate, set it to null so a different codec can be installed and try validating another chunk. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31750 60cd2ccc-2b05-0410-9566-da273a940bff | 10 May 2012, 10:34:06 UTC |
| 85ef9f8 | Kevin C. Dorf | 09 May 2012, 19:07:00 UTC | display class name with exceptions in SoftMode. Just exception, not throwable any more. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31747 60cd2ccc-2b05-0410-9566-da273a940bff | 09 May 2012, 19:07:00 UTC |
| 6e6065f | Fabien Campagne | 09 May 2012, 18:58:50 UTC | Validate the chunk content past the size to make sure we did not reach a spurious boundary. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31746 60cd2ccc-2b05-0410-9566-da273a940bff | 09 May 2012, 18:58:50 UTC |
| 89f9b3b | Kevin C. Dorf | 09 May 2012, 17:46:03 UTC | One too many closes, the alignment iterator closes the writer so it doesn't work to close the writer in SortMode. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31745 60cd2ccc-2b05-0410-9566-da273a940bff | 09 May 2012, 17:46:03 UTC |
| 256fa23 | Kevin C. Dorf | 09 May 2012, 16:46:29 UTC | Two more missed closes in SortMode() in the first pass (single section) sort. git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby@31744 60cd2ccc-2b05-0410-9566-da273a940bff | 09 May 2012, 16:46:29 UTC |
